There are several books I would recommend:
1) Database Design and Implementation by Edward Sciore:
This book teaches RDBMS from conceptual perspective up to implementing your own RDBMS (using Java albeit).
2) OS Design XINU Approach (look for the PC edition)
3) Bunch of UNIX/Linux books
- The Design of the UNIX Operating System (M. Bach)
- Design and Implementation of BSD 4.4/FreeBSD 5.2
Unfortunately I don't think jumping to the most recent Linux kernel books would be feasible.
4) Look for any books that teaches both concepts and provide simple implementation of the said concepts.
Find a book that teaches the concept of Graphics Pipeline and try to implement it yourself: http://www.viznet.ac.uk/files/d39pipeline.gif
5) Check out the Java SDK (the actual implementation, not how to use the library) and HotSpot VM guides
- Concurrent, NIO/IO, Networking, Threading
- Garbage Collection, optimization, Class Loading, etc
I think the more you learn, exercise, and understand many system designs out there could help you to build your own "intuition" in the future.
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